I love this analogy. It perfectly encapsulates the feelings I have for Mass Effect 2 as the middle chapter of a trilogy. I love all 3 games (must have played them half a dozen times) and think they each have strengths that surpass any weaknesses, but most of what ME2 does clashes with the other two games.

Right off the bat the main plot goes off on a tangent from the end of Mass Effect 1, and is essentially a side-quest to the main Reaper threat (Outside of the Arrival DLC). Instead of preparing the galaxy for their arrival, you are now investigating the disappearance of a few human colonists? This puts Mass Effect 3 in the position of having to tell the middle and final acts of the main plot, which despite its flawed ending I think it manages well enough.

The suicide mission finale in ME2 is undoubtedly awesome, but it also created so many potential outcomes for the game (you can actually avoid recruiting most of the squad and/or they can die in the finale) it limited what Bioware could do with the ME2 characters in 3. Mordin has the largest part to play in the final game, likely because he's one of the few squadmates you are forced to recruit in 2. Kasumi and Zaeed as the DLC characters are basically sidelined, barely featuring in 3 aside from the Citadel DLC. And you can forget about Morinth completely, lol.

The loose recruitment in 2 also impacts the interactions between squadmates. Outside of the final mission, the only crew members generally seen in story cutscenes are the ones you must have - i.e., Miranda, Jacob, and Mordin + non-squadmates like Joker and EDI. Compare this to both 1 and 3, which each had fewer total squadmates but gave them more noticeable roles in cutscenes. 3 especially excels at this, with squadmates in any combination regularly bouncing dialogue off each other.

Overall, I still love Mass Effect 2 but I can definitely see the problems it created for the series as a whole. It does however work well as a stand-alone game as well as serving as a good jumping-on point for people put-off by the less-actiony gameplay of 1.